AML datasets

Note: Validation mice also available via Haemdata/Ondrive. See X for more details.

First, we need to setup the pin-board and download the mouse datasets.

library(haemdata)
use_pinboard("devel")

all_mice <- get_pin("mmu_mrna_all_mice_GENCODEm28_HLT_qc.rds")
se <- subset(all_mice,
    select = grepl("2016", SummarizedExperiment::colData(all_mice)$batch)
)

pca <- pca_se(se)
pca$biplot

pca$pairs_plot

pca$correlation_plot

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2016")

se <- subset(all_mice,
    select = grepl("AML.mRNA.2018.all_samples", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)
pca$biplot

pca$pairs_plot

pca$correlation_plot

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2018")

se <- subset(all_mice,
    select = grepl("AML.mRNA.2020", SummarizedExperiment::colData(all_mice)$cohort)
)
se <- subset(se,
    select = grepl("PBMC", SummarizedExperiment::colData(se)$tissue)
)

pca <- pca_se(se)
pca$biplot

pca$pairs_plot

pca$correlation_plot

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2020")

se <- subset(all_mice,
    select = grepl("RxGroup", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)
pca$biplot

pca$pairs_plot

pca$correlation_plot

metadata_mmu |>
plot_cohort_survival("RxGroup")

se <- subset(all_mice,
    select = grepl("AML.scRNAseq.2022", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)
pca$biplot

pca$pairs_plot

pca$correlation_plot

se <- subset(all_mice,
    select = ("BM" == SummarizedExperiment::colData(all_mice)$tissue)
)
se <- subset(se,
    select = grepl("AML", SummarizedExperiment::colData(se)$cohort)
)

pca <- pca_se(se)
pca$biplot

pca$pairs_plot

pca$correlation_plot

First, we need to setup the pin-board from which well retrieve the human datasets

City of Hope Biobank FLT3 patients

Include some background info on these samples, IRB etc

library(haemdata)
use_pinboard("devel")
se <- get_pin("hsa_mrna_flt3_GENCODEr40_qc.rds")

pca <- pca_se(se, col_by = "patient_id")
pca$biplot

pca$pairs_plot

pca$correlation_plot

Kim et al 2020 Sci Rep DOI

Bioproject: PRJEB27973

se <- get_pin("hsa_mrna_kim_GENCODEr40_qc.rds")

pca <- pca_se(se, col_by = "timepoint")
pca$biplot

pca$pairs_plot

pca$correlation_plot